scholarly journals Grandparent inference from genetic data: The potential for parentage-based tagging programs to identify offspring of hatchery strays

2021 ◽  
Author(s):  
Thomas A Delomas ◽  
Matthew Campbell
Keyword(s):  
False Negative ◽  
Genetic Data ◽  
R Package ◽  
Error Rates ◽  
Nucleotide Polymorphisms ◽  
Negative Effects ◽  
Single Nucleotide ◽  
Natural Origin ◽  
False Negative Error ◽  
In The Wild

Fisheries managers routinely use hatcheries to increase angling opportunity. Many hatcheries operate as segregated programs where hatchery-origin fish are not intended to spawn with natural-origin conspecifics in order to prevent potential negative effects on the natural-origin population. Currently available techniques to monitor the frequency with which hatchery-origin strays successfully spawn in the wild rely on either genetic differentiation between the hatchery- and natural-origin fish or extensive sampling of fish on the spawning grounds. We present a method to infer grandparent-grandchild trios using only genotypes from two putative grandparents and one putative grandchild. We developed estimators of false positive and false negative error rates and showed that genetic panels containing 500 - 700 single nucleotide polymorphisms or 200 - 300 microhaplotypes are expected to allow application of this technique for monitoring segregated hatchery programs. We discuss the ease with which this technique can be implemented by pre-existing parentage-based tagging programs and provide an R package that applies the method.

EpiPen: An R Package to Investigate Two-Locus Epistatic Models

2014 ◽  
Vol 17 (4) ◽  
Author(s):  
Raymond K. Walters ◽  
Charles Laurin ◽  
Gitta H. Lubke
Keyword(s):  
Power Analysis ◽  
R Package ◽  
Simulation Studies ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Epistatic Interactions ◽  
Model Interpretation ◽  
Genome Wide ◽  
Using Data ◽  
Power Analyses

Epistasis is a growing area of research in genome-wide studies, but the differences between alternative definitions of epistasis remain a source of confusion for many researchers. One problem is that models for epistasis are presented in a number of formats, some of which have difficult-to-interpret parameters. In addition, the relation between the different models is rarely explained. Existing software for testing epistatic interactions between single-nucleotide polymorphisms (SNPs) does not provide the flexibility to compare the available model parameterizations. For that reason we have developed an R package for investigating epistatic and penetrance models, EpiPen, to aid users who wish to easily compare, interpret, and utilize models for two-locus epistatic interactions. EpiPen facilitates research on SNP-SNP interactions by allowing the R user to easily convert between common parametric forms for two-locus interactions, generate data for simulation studies, and perform power analyses for the selected model with a continuous or dichotomous phenotype. The usefulness of the package for model interpretation and power analysis is illustrated using data on rheumatoid arthritis.

scholarly journals Differences in mate pairings of hatchery and natural origin coho salmon inferred from offspring genotypes

2021 ◽  
Author(s):  
H L Auld ◽  
D P Jacobson ◽  
A C Rhodes ◽  
M A Banks
Keyword(s):  
Mate Choice ◽  
Captive Breeding ◽  
Population Genomics ◽  
Coho Salmon ◽  
Genotyping By Sequencing ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Natural Origin ◽  
In Captivity ◽  
Genetic Level

Abstract Captive breeding can affect how sexual selection acts on subsequent generations. One context where this is important is in fish hatcheries. In many salmon hatcheries, spawning is controlled artificially and offspring are reared in captivity before release into the wild. While previous studies have suggested that hatchery and natural origin fish may make different mate choice decisions, it remains to be determined how hatchery fish may be making different mate choice decisions compared to natural origin fish at a genetic level. Using genotyping-by-sequencing (GBS), we identify single nucleotide polymorphisms (SNPs) associated with variation in mate pairings from a natural context involving hatchery and natural origin coho salmon (Oncorhynchus kisutch). In both natural origin and hatchery mate pairs, we observed more SNPs with negative assortment, than positive assortment. However, only 3% of the negative assortment SNPs were shared between the two mating groups, and 1% of the positive assortment SNPs were shared between the two mating groups, indicating divergence in mating cues between wild and hatchery raised salmon. These findings shed light on mate choice in general and may have important implications in the conservation management of species as well as for improving other captive breeding scenarios. There remains much to discover about mate choice in salmon and research described here reflects our intent to test the potential of ongoing advances in population genomics to develop new hatchery practices that may improve the performance of hatchery offspring, lessening the differences and thus potential impacts upon wild stocks.

Error Rates in Competency Testing When Test Retaking Is Permitted

1990 ◽  
Vol 15 (1) ◽  
pp. 39-52 ◽  
Author(s):  
Huynh Huynh
Keyword(s):  
Conditional Probability ◽  
False Positive ◽  
False Negative ◽  
Error Rates ◽  
Rasch Models ◽  
Positive Error ◽  
False Positive Error ◽  
Competency Testing ◽  
Negative Error ◽  
False Negative Error

False positive and false negative error rates are studied for competency testing where examinees are permitted to retake the test if they fail to pass. Formulae are provided for the beta-binomial and Rasch models, and estimates based on these two models are compared for several typical situations. Although Rasch estimates are expected to be more accurate than beta-binomial estimates, differences among them are found not to be substantial in a number of practical situations. Under relatively general conditions and when test retaking is permitted, the probability of making a false negative error is zero. Under the same situation, and given that an examinee is a true nonmaster, the conditional probability of making a false positive error for this examinee is one.

Errors in prostate core biopsy diagnosis in an era of specialisation and double reporting

2020 ◽  
pp. jclinpath-2020-206726
Author(s):  
Cornelia Margaret Szecsei ◽  
Jon D Oxley
Keyword(s):  
Error Rate ◽  
False Positive ◽  
Core Biopsy ◽  
False Negative ◽  
Diagnostic Error ◽  
Error Rates ◽  
False Positive Error ◽  
Biopsy Diagnosis ◽  
False Negative Error ◽  
False Positive Error Rate

AimTo examine the effects of specialist reporting on error rates in prostate core biopsy diagnosis.MethodBiopsies were reported by eight specialist uropathologists over 3 years. New cancer diagnoses were double-reported and all biopsies were reviewed for the multidisciplinary team (MDT) meeting. Diagnostic alterations were recorded in supplementary reports and error rates were compared with a decade previously.Results2600 biopsies were reported. 64.1% contained adenocarcinoma, a 19.7% increase. The false-positive error rate had reduced from 0.4% to 0.06%. The false-negative error rate had increased from 1.5% to 1.8%, but represented fewer absolute errors due to increased cancer incidence.ConclusionsSpecialisation and double-reporting have reduced false-positive errors. MDT review of negative cores continues to identify a very low number of false-negative errors. Our data represents a ‘gold standard’ for prostate biopsy diagnostic error rates. Increased use of MRI-targeted biopsies may alter error rates and their future clinical significance.

scholarly journals High resolution analysis of cervical cells--a progress report.

1977 ◽  
Vol 25 (7) ◽  
pp. 689-695 ◽  
Author(s):  
R S Poulsen ◽  
L H Oliver ◽  
R L Cahn ◽  
C Louis ◽  
G Toussaint
Keyword(s):  
High Resolution ◽  
False Positive ◽  
False Negative ◽  
Error Rates ◽  
Cell Segmentation ◽  
Negative Error ◽  
False Negative Error ◽  
High Resolution Analysis ◽  
Resolution Analysis ◽  
Cervical Cells

This paper presents preliminary results of research toward the development of a high resolution analysis stage for a dual resolution image processing-based prescreening device for cervical cytology. Experiments using both manual and automatic methods for cell segmentation are described. In both cases, 1500 cervical cells were analyzed and classified as normal or abnormal (dysplastic or malignant) using a minimum Mahalanobis distance classifier with eight subclasses of normal cells, and five subclasses of abnormal cells. With manual segmentation, false positive and false negative error rates of 2.98 and 7.73% were obtained. Similar experiments using automatic cell segmentation methods yielded false positive and false negative error rates of 3.90 and 11.56%, respectively. In both cases, independent training and testing data were used.

scholarly journals 11 Million SNP Reference Profiles for Identity Searching Across Ethnicities, Kinship, and Admixture

2018 ◽  
Author(s):  
Brian S. Helfer ◽  
Darrell O. Ricke
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
High Throughput ◽  
Family Relationships ◽  
In Silico ◽  
High Throughput Sequencing ◽  
Genetic Data ◽  
Nucleotide Polymorphisms ◽  
Mixture Analysis ◽  
Single Nucleotide ◽  
Public Repositories

AbstractHigh throughput sequencing (HTS) of single nucleotide polymorphisms (SNPs) provides additional applications for DNA forensics including identification, mixture analysis, kinship prediction, and biogeographic ancestry prediction. Public repositories of human genetic data are being rapidly generated and released, but the majorities of these samples are de-identified to protect privacy, and have little or no individual metadata such as appearance (photos), ethnicity, relatives, etc. A reference in silico dataset has been generated to enable development and testing of new DNA forensics algorithms. This dataset provides 11 million SNP profiles for individuals with defined ethnicities and family relationships spanning eight generations with admixture for a panel with 39,108 SNPs.

scholarly journals Smart Pooling: AI-Powered COVID-19 Informative Group Testing

2021 ◽  
Author(s):  
Maria Escobar ◽  
Guillaume Jeanneret ◽  
Laura Bravo-Sánchez ◽  
Angela Castillo ◽  
Catalina Gómez ◽  
...  
Keyword(s):  
Machine Learning ◽  
False Negative ◽  
Group Testing ◽  
Error Rates ◽  
Molecular Testing ◽  
Proof Of Concept ◽  
Efficiency Gains ◽  
Automated Method ◽  
Sociodemographic Data ◽  
False Negative Error

Abstract Massive molecular testing for COVID-19 has been pointed out as fundamental to moderate the spread of the pandemic. Pooling methods can enhance testing efficiency, but they are viable only at low incidences of the disease. We propose Smart Pooling, a machine learning method that uses clinical and sociodemographic data from patients to increase the efficiency of informed Dorfman testing for COVID-19 by arranging samples into all-negative pools. To do this, we ran an automated method to train numerous machine learning models on a retrospective dataset from more than 8,000 patients tested for SARS-CoV-2 from April to July 2020 in Bogotá, Colombia. We estimated the efficiency gains of using the predictor to support Dorfman testing by simulating the outcome of tests. We also computed the attainable efficiency gains of non-adaptive pooling schemes mathematically. Moreover, we measured the false-negative error rates in detecting the ORF1ab and N genes of the virus in RT-qPCR dilutions. Finally, we presented the efficiency gains of using our proposed pooling scheme on proof-of-concept pooled tests. We believe Smart Pooling will be efficient for optimizing massive testing of SARS-CoV-2.

scholarly journals Single-nucleotide polymorphisms in FABP4 gene associated with growth traits in Egyptian sheep

2020 ◽  
Vol 13 (6) ◽  
pp. 1126-1132
Author(s):  
Heba Ibrahim Shafey ◽  
Karima Fathy Mahrous ◽  
Amal Ahmed Mohamed Hassan ◽  
Hossam Eldin Rushdi ◽  
Mohamed Abd El-Aziz Mohamed Ibrahim
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Growth Traits ◽  
Average Daily Gain ◽  
Correlation Coefficients ◽  
Nucleotide Polymorphisms ◽  
Negative Effects ◽  
Single Nucleotide ◽  
Fatty Acid Binding ◽  
Sheep Breeds ◽  
Intron 1

Aim: The present study was performed to assess the association of single-nucleotide polymorphisms (SNPs) in the fatty acid-binding protein 4 (FABP4) gene with birth weight (BW), final weight (FW), and average daily gain (ADG) in three Egyptian sheep breeds. Materials and Methods: Genomic DNA was extracted from the blood samples of 50 male and female individuals representing Ossimi, Rahmani, and Barki sheep breeds. A 407 bp nucleotide (nt) segment from the first intron of FABP4 was amplified by polymerase chain reaction, sequenced, and analyzed in the different samples. Results: Sequence analysis of the determined segment (407 bp) revealed four SNPs (all transition types) at nt position 372 (CP011894.1:g.57605471) A>G, nt position 211 (CP011894.1:g.57605632) A>G, nt position 143 (CP011894.1:g.57605700) T>C, and nt position 111 (CP011894.1:g.57605732) T>C. The allelic and genotypic frequencies for the identified SNPs in the sheep breeds were calculated. At nt positions 372 and 211, two alleles were identified (A and G). Only two genotypes were present at nt position 372 (AA and AG), while three genotypes were present at nt position 211 (AA, AG, and GG). Two alleles (T and C) and three identified genotypes (TT, TC, and CC) were detected at nt positions 143 and 111. Analysis of the results revealed that AA genotype at nt position 372 is associated with higher estimates for BW, FW, and ADG when compared to all the other genotypes. Very high correlation coefficients were found between the genotypes 143-TT and 111-TT and also between 143-TC and 111-TC. The genotypes 372-AG, 211-GG, 211-AA, 143-TT, 143-CC, 111-TT, 111-TC, and 111-CC were associated with negative effects on BW, FW, and ADG. Conclusion: The detection of four SNPs in a partial sequence of the Egyptian ovine FABP4 gene intron 1 reflected that this gene harbors substantial diversity. In addition, a novel SNP at nt position 372 (CP011894.1:g.57605471) A>G was associated with higher estimates for BW, FW, and ADG.

Association of PPARG Gene Polymorphisms Pro12Ala with Type 2 Diabetes Mellitus: A Meta-analysis

2019 ◽  
Vol 15 (4) ◽  
pp. 277-283 ◽  
Author(s):  
Junyan Li ◽  
Xiaohong Niu ◽  
JianBo Li ◽  
Qingzhong Wang
Keyword(s):  
Publication Bias ◽  
Chinese Population ◽  
Meta Analysis ◽  
Genetic Data ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genetic Studies ◽  
Combined Analysis ◽  
Pparg Gene

Background:Previous studies suggested that the single nucleotide polymorphisms of Pro12Ala located within the PPARG gene were significantly associated with the T2DM. Recently, the genetic studies on Pro12Ala were conducted in the different ethnic groups and the results of each study were shown to be inconsistent. Moreover, the systematic review has not been updated since 2000.Objective:To further validate the risk of Pro12Ala for T2DM disease based on the genetic data.Methods:The genetic studies on the Pro12Ala in the T2DM were searched in the PubMed and PMC database from January 2000 to October 2017. The meta-analysis was conducted with the CMA software.Results:The meta-analysis collected 14 studies including 20702 cases and 36227 controls. The combined analysis of all studies found that Pro12Ala was shown to be significantly associated with T2DM and the Ala allele played the increasing risks for the disease. Nevertheless, publication bias was detected in the combined analysis. The subgroup analysis indicated that Pro12Ala was found to be significant in the Caucasian and Chinese population. There was no heterogeneity and publication bias in these two groups.Conclusion:The meta-analysis confirmed the evidence that the Pro12Ala was the susceptible variant for the decreasing risks for the T2DM

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